I am new to R and the ldscr function. I am trying to run cross-trait LDSC for two munged datasets. But I kept getting the following abnormal values:
Theoretically, the genetic correlation (rg) is between -1 and 1. However, in my results, there are some cases where rg is greater than 1 or less than -1. Is this a problem with my data or a flaw in the R package?
The data input format is as required, where dt1 and dt2 are two dataframes with 5 columns (SNP, A1, A2, N, Z):
Dear Sir/Madam,
I am new to R and the ldscr function. I am trying to run cross-trait LDSC for two munged datasets. But I kept getting the following abnormal values:
Theoretically, the genetic correlation (rg) is between -1 and 1. However, in my results, there are some cases where rg is greater than 1 or less than -1. Is this a problem with my data or a flaw in the R package?
The data input format is as required, where dt1 and dt2 are two dataframes with 5 columns (SNP, A1, A2, N, Z):
rg_res<-ldscr::ldsc_rg( munged_sumstats = list( "liver"=dt1, "immune"=dt2), ancestry="EUR")
Please kindly advise! Thank you very much.
Best regards,
ahj